3v79

Structure of human Notch1 transcription complex including CSL, RAM, ANK, and MAML-1 on HES-1 promoter DNA sequence

Method: X-RAY DIFFRACTION Dmax: 106.3 Å Quality: GOOD

1. Protein Identity and Related Structures Protein Identity & Related Structures

Neurogenic locus notch homolog protein 1

Homo sapiens

UniProt P46531

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 4 DNA 2 PDB declaration: hexameric(6) Consistent with all polymer counts Chain K; UniProt 1872–2126 Not recorded Recombining binding protein suppressor of hairless × 1 (Q06330) Mastermind-like protein 1 × 1 (Q92585) ;DNA 5'-D(*GP*TP*TP*AP*CP*TP*GP*TP*GP*GP*GP*AP*AP*AP*GP*AP*AP*A)-3' ; × 1 ;DNA 5'-D(*TP*TP*TP*CP*TP*TP*TP*CP*CP*CP*AP*CP*AP*GP*TP*AP*AP*C)-3' ; × 1 RAM × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.9;298 K;6% PEG 3350, 5% Ethylene glycol, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 3.85 Å R-free 0.245

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

27 other PDB entries and 35 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NOTC1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain K; PDBConstruct 2–256; UniProt 1872–2126

Recombining binding protein suppressor of hairless

Homo sapiens

UniProt Q06330

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 4 DNA 2 PDB declaration: hexameric(6) Consistent with all polymer counts Chain C; UniProt 23–449 Not recorded Neurogenic locus notch homolog protein 1 × 1 (P46531) Mastermind-like protein 1 × 1 (Q92585) ;DNA 5'-D(*GP*TP*TP*AP*CP*TP*GP*TP*GP*GP*GP*AP*AP*AP*GP*AP*AP*A)-3' ; × 1 ;DNA 5'-D(*TP*TP*TP*CP*TP*TP*TP*CP*CP*CP*AP*CP*AP*GP*TP*AP*AP*C)-3' ; × 1 RAM × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.9;298 K;6% PEG 3350, 5% Ethylene glycol, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 3.85 Å R-free 0.245

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

3 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SUH_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain C; PDBConstruct 2–428; UniProt 23–449

Mastermind-like protein 1

Homo sapiens

UniProt Q92585

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 4 DNA 2 PDB declaration: hexameric(6) Consistent with all polymer counts Chain M; UniProt 13–74 Not recorded Neurogenic locus notch homolog protein 1 × 1 (P46531) Recombining binding protein suppressor of hairless × 1 (Q06330) ;DNA 5'-D(*GP*TP*TP*AP*CP*TP*GP*TP*GP*GP*GP*AP*AP*AP*GP*AP*AP*A)-3' ; × 1 ;DNA 5'-D(*TP*TP*TP*CP*TP*TP*TP*CP*CP*CP*AP*CP*AP*GP*TP*AP*AP*C)-3' ; × 1 RAM × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.9;298 K;6% PEG 3350, 5% Ethylene glycol, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 3.85 Å R-free 0.245

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MAML1_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain M; PDBConstruct 2–63; UniProt 13–74

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 3v79

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3v79
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3v79
Deposition date deposition_date2011-12-20
Structure title titleStructure of human Notch1 transcription complex including CSL, RAM, ANK, and MAML-1 on HES-1 promoter DNA sequence
Keywords keywordsbeta-trefoil, ankyrin, transcription activation, DNA Binding, transcription-DNA complex; transcription/DNA
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier31.36
Radius of gyration Rg (electron density) rg_electron30.03
Forward intensity I(0) i0162863000.00
Molecular weight molecular_weight92091.0 kDa
Excluded volume excluded_volume111380 ų
Envelope volume envelope_volume148210 ų
Hydration-shell volume shell_volume40209 ų
Envelope diameter envelope_diameter112.9
Shell Rg shell_rg38.06
Envelope Rg envelope_rg29.93
Shape Rg shape_rg29.99
Total Rg total_rg30.78
Total atoms total_atoms6421
Residues n_residues752
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax106.3
Rg (real space) rg_real31.24
Rg uncertainty (real space) rg_real_error0.68
I(0) (real space) i0_real1.6290e+08
I(0) uncertainty (real space) i0_real_error2.4030e+06
Rg (reciprocal space) rg_reciprocal31.29
I(0) (reciprocal space) i0_reciprocal162900000.0000
Solution quality estimate total_estimate0.8840
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary39.6
Skewness Skewness skewness0.207
Kurtosis Kurtosis kurtosis-0.395
Angular range angular_range— – 0.2550 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha22050000.0000
Real-space data points n_real_points52
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.836; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.989

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 5 domains

CATH v4.4 (5 domains)

Domain ID domain_id3v79C01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily1450 — LAG1, DNA binding domain
Domain ID domain_id3v79C02
Class class2 — Mainly Beta
Architecture architecture80 — Trefoil
Topology topology10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily50
Domain ID domain_id3v79C03
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3v79K00
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily20 — Ankyrin repeat-containing domain
Domain ID domain_id3v79M00
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily970

8. Citations (1)

9. Files and Curves (10)